[AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide

From: Jiaan Zhu via AMBER <amber.ambermd.org>
Date: Sun, 4 Sep 2022 12:46:32 +0200


I’m trying to generate parameters of an artificial nucleotide by the following steps:
1. Download 1WA.cif file from PDB
2. antechamber -fi ccif -i 1WA.cif -bk 1WA -fo ac -o 1wa.ac -c bcc -at amber
3. prepgen -i 1wa.ac -o 1wa.prepin -m 1wa.mc -rn 1WA
4.parmchk2 -i 1wa.prepin -f prepi -o frcmod.1wa -a Y -p $AMBERHOME/dat/leap/parm/parm10.dat

There’s an error in the step 4: $AMBERHOME/bin/parmchk2: line 4: 666869 Segmentation fault (core dumped) $AMBERHOME/bin/to_be_dispatched/parmchk2 "$@“

Does anyone know how to fix this problem? The 1WA.cif, 1wa.prepin and 1wa.mc files are attached.

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Received on Sun Sep 04 2022 - 04:00:02 PDT
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